Additional file 1: of NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis

Supplementary materials including the classification of enrichment analysis methods, the parameter sensitivity analysis, the additional simulation results, and the description of gene expression datasets, GO annotation data, and active gene lists used in real data applications. (PDF 1385 kb

Link communities of three artifical networks.

<p>(A) The network consists of five overlapping communities. Nodes 1, 7, 12, 16 are overlapping nodes; (B) The network consists of two overlapping communities. Nodes 1 and 2 are overlapping nodes that belong to the two communities, and link (1, 2) belongs to the two communities as well; (C) The network consists of two overlapping cliques and the overlapped subgraph is a 3-clique.</p

Link communities of some real-world networks.

<p>(A) The Karate club network; (B) The word association network; (C) The co-appearance network.</p

Link communities of three networks of heterogeneous cliques.

<p>(A) The ring network of heterogeneous cliques. Each community is a clique, and two adjacent communities are connected by one node. (B) The ring network of overlapping heterogeneous cliques. Each community is a clique, and two adjacent communities are connected by one node or one link. (C) The tree network of heterogeneous cliques. Each community is a clique, and two adjacent communities are overlapped by one node <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083739#pone.0083739-Ahn1" target="_blank">[11]</a>.</p

The network in Ref. [11] can be correctly partitioned into three communities by our model, and the objective function value is 1.

<p>The network in Ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083739#pone.0083739-Ahn1" target="_blank">[11]</a> can be correctly partitioned into three communities by our model, and the objective function value is 1.</p

The parameters used in the GA algorithm for solving the link community detection problem on networks in Figure 2.

<p>The parameters used in the GA algorithm for solving the link community detection problem on networks in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083739#pone-0083739-g002" target="_blank">Figure 2</a>.</p

Three different partition results of a tree network.

<p>(A) Correct partition. (B,C) Two counter-intuitive partitions. The red links and their adjacent nodes constitute a community, the blue links and their adjacent nodes form another community. The black node is overlapped.</p

The overlaps of domain-domain interactions predicted by APMM, DPEA and PE with iPfam

<p><b>Copyright information:</b></p><p>Taken from "Analysis on multi-domain cooperation for predicting protein-protein interactions"</p><p>http://www.biomedcentral.com/1471-2105/8/391</p><p>BMC Bioinformatics 2007;8():391-391.</p><p>Published online 16 Oct 2007</p><p>PMCID:PMC2222654.</p><p></p